RNA-Guided Targeting of Genetic and Epigenomic Regulatory Proteins to Specific Genomic Loci

ABSTRACT

Methods and constructs for RNA-guided targeting of heterologous functional domains such as transcriptional activators to specific genomic loci.

CLAIM OF PRIORITY

This application is a divisional of U.S. patent application Ser. No.16/535,199, filed Aug. 8, 2019, which is a continuation of U.S. patentapplication Ser. No. 14/775,869, filed Sep. 14, 2015, now U.S. Pat. No.10,378,027, which is a U.S. National Phase Application under 35 U.S.C. §371 of International Patent Application No. PCT/US2014/027335, filed onMar. 14, 2014, which claims the benefit of U.S. Patent Application Ser.Nos. 61/799,647, filed on Mar. 15, 2013; 61/838,178, filed on Jun. 21,2013; 61/838,148, filed on Jun. 21, 2013; and 61/921,007, filed on Dec.26, 2013. The entire contents of the foregoing are hereby incorporatedby reference.

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under Grant No.DP1GM105378 awarded by the National Institutes of Health andW911NF-11-2-0056 awarded by the Defense Advanced Research ProjectsAgency (DARPA) of the Department of Defense. The Government has certainrights in the invention.

SEQUENCE LISTING

This application contains a Sequence Listing that has been submittedelectronically as an ASCII text file named “Sequence_Listing.txt.” TheASCII text file, created on Oct. 5, 2021, is 133 KB in size. Thematerial in the ASCII text file is hereby incorporated by reference inits entirety.

TECHNICAL FIELD

This invention relates to methods and constructs for RNA-guidedtargeting of genetic and epigenomic regulatory proteins, e.g.,transcriptional activators, histone modification enzymes, DNAmethylation modifiers, to specific genomic loci.

BACKGROUND

Clustered Regulatory Interspaced Short Palindromic Repeats (CRISPR), andCRISPR-associated (cas) genes, referred to as CRISPR/Cas systems, areused by various bacteria and archaea to mediate defense against virusesand other foreign nucleic acid. These systems use small RNAs to detectand silence foreign nucleic acids in a sequence-specific manner.

Three types of CRISPR/Cas systems have been described (Makarova et al.,Nat. Rev. Microbiol. 9, 467 (2011); Makarova et al., Biol. Direct 1, 7(2006); Makarova et al., Biol. Direct 6, 38 (2011)). Recent work hasshown that Type II CRISPR/Cas systems can be engineered to directtargeted double-stranded DNA breaks in vitro to specific sequences byusing a single “guide RNA” with complementarity to the DNA target siteand a Cas9 nuclease (Jinek et al., Science 2012; 337:816-821). Thistargetable Cas9-based system also works in cultured human cells (Mali etal., Science. 2013 Feb. 15; 339(6121):823-6; Cong et al., Science. 2013Feb. 15; 339(6121):819-23) and in vivo in zebrafish (Hwang and Fu etal., Nat Biotechnol. 2013 March; 31(3):227-9) for inducing targetedalterations into endogenous genes.

SUMMARY

At least in part, the present invention is based on the development of afusion protein including a heterologous functional domain (e.g., atranscriptional activation domain) fused to a Cas9 nuclease that has hadits nuclease activity inactivated by mutations (also known as “dCas9”).While published studies have used guide RNAs to target catalyticallyactive and inactive Cas9 nuclease proteins to specific genomic loci, nowork has yet adapted the use of this system to recruit additionaleffector domains. This work also provides the first demonstration of anRNA-guided process that results in an increase (rather than a decrease)in the level of expression of a target gene.

In addition, the present disclosure provides the first demonstrationthat multiplex gRNAs can be used to bring multiple dCas9-VP64 fusions toa single promoter, thereby resulting in synergistic activation oftranscription.

Thus, in a first aspect, the invention provides fusion proteinscomprising a catalytically inactive CRISPR associated 9 (dCas9) proteinlinked to a heterologous functional domain (HFD) that modifies geneexpression, histones, or DNA, e.g., transcriptional activation domain,transcriptional repressors (e.g., silencers such as HeterochromatinProtein 1 (HP1), e.g., HP1α or HP1β, or a transcriptional repressiondomain, e.g., Krueppel-associated box (KRAB) domain, ERF repressordomain (ERD), or mSin3A interaction domain (SID)), enzymes that modifythe methylation state of DNA (e.g., DNA methyltransferase (DNMT) orTen-Eleven Translocation (TET) proteins, e.g., TET1, also known as TetMethylcytosine Dioxygenase 1), or enzymes that modify histone subunit(e.g., histone acetyltransferases (HAT), histone deacetylases (HDAC), orhistone demethylases). In some embodiments, the heterologous functionaldomain is a transcriptional activation domain, e.g., a transcriptionalactivation domain from VP64 or NF-κB p65; an enzyme that catalyzes DNAdemethylation, e.g., a TET; or histone modification (e.g., LSD1, histonemethyltransferase, HDACs, or HATs) or a transcription silencing domain,e.g., from Heterochromatin Protein 1 (HP1), e.g., HP1α or HP1β; or abiological tether, e.g., CRISPR/Cas Subtype Ypest protein 4 (Csy4), MS2,or lambda N protein.

In some embodiments, the catalytically inactive Cas9 protein is from S.pyogenes.

In some embodiments, the catalytically inactive Cas9 protein comprisesmutations at comprises mutations at D10, E762, H983, or D986; and atH840 or N863, e.g., at D10 and H840, e.g., D10A or D10N and H840A orH840N or H840Y.

In some embodiments, the heterologous functional domain is linked to theN terminus or C terminus of the catalytically inactive Cas9 protein,with an optional intervening linker, wherein the linker does notinterfere with activity of the fusion protein.

In some embodiments, the fusion protein includes one or both of anuclear localization sequence and one or more epitope tags, e.g., c-myc,6His, or FLAG tags, on the N-terminus, C-terminus, or in between thecatalytically inactive CRISPR associated 9 (Cas9) protein and theheterologous functional domain, optionally with one or more interveninglinkers.

In further aspect, the invention provides nucleic acids encoding thefusion proteins described herein, as well as expression vectorsincluding the nucleic acids, and host cells expressing the fusionproteins.

In an additional aspect, the invention provides methods for increasingexpression of a target gene in a cell. The methods include expressing aCas9-HFD fusion protein as described herein in the cell, e.g., bycontacting the cell with an expression vector including a sequenceencoding the fusion protein, and also expressing in the cell one or moreguide RNAs with complementarity directed to the target gene, e.g., bycontacting the cell with one or more expression vectors comprisingnucleic acid sequences encoding one or more guide RNAs.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Methods and materials aredescribed herein for use in the present invention; other, suitablemethods and materials known in the art can also be used. The materials,methods, and examples are illustrative only and not intended to belimiting. All publications, patent applications, patents, sequences,database entries, and other references mentioned herein are incorporatedby reference in their entirety. In case of conflict, the presentspecification, including definitions, will control.

Other features and advantages of the invention will be apparent from thefollowing detailed description and figures, and from the claims.

DESCRIPTION OF DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

FIG. 1A is a schematic illustration showing a single guide RNA (sgRNA)recruiting Cas9 nuclease to a specific DNA sequence and therebyintroducing targeted alterations. The sequence of the guide RNA shown is

(SEQ ID NO: 9) GGAGCGAGCGGAGCGGUACAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCG

FIG. 1B is a schematic illustration showing a longer version of thesgRNA used to recruit Cas9 nuclease to a specific DNA sequence and tothereby introduce targeted alterations. The sequence of the guide RNAshown is

(SEQ ID NO: 10) GGAGCGAGCGGAGCGGUACAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUU UU.

FIG. 1C is a schematic illustration showing a Cas9 protein containingD10A and H840A mutations to render the nuclease portion of the proteincatalytically inactive, fused to a transcriptional activation domain andrecruited to a specific DNA sequence by a sgRNA. The sequence of theguide RNA shown is

(SEQ ID NO: 10) GGAGCGAGCGGAGCGGUACAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUU UU.

FIG. 1D is a schematic depicting recruitment of dCas9-VP64 fusionprotein to a specific genomic target sequence by a chimeric sgRNA.

FIG. 1E is a diagram illustrating the positions and orientations of 16sgRNAs targeted to the endogenous human VEGFA gene promoter. Smallhorizontal arrows represent the first 20 nts of the gRNA complementaryto the genomic DNA sequence with the arrow pointing 5′ to 3′. Grey barsindicate DNaseI hypersensitive sites previously defined in human 293cells (Liu et al., J Biol Chem. 2001 Apr. 6; 276(14):11323-34), numberedrelative to the transcription start site (right-angle arrow).

FIG. 2A is a bar graph showing activation of VEGFA protein expression in293 cells by various sgRNAs, each expressed with (grey bars) or without(black bars) dCas9-VP64. Fold-activation of VEGFA was calculatedrelative to the off-target sgRNA control as described in Methods. Eachexperiment was performed in triplicate and error bars represent standarderrors of the mean. Asterisks indicate samples that are significantlyelevated above the off-target control as determined by a paired,one-sided t-test (p<0.05).

FIG. 2B is a bar graph showing multiplex sgRNA expression inducessynergistic activation of VEGFA protein expression by dCas9-VP64protein. Fold-activation of VEGFA protein in 293 cells in which theindicated combinations of sgRNAs were co-expressed with dCas9-VP64 isshown. Note that in all of these experiments the amount of eachindividual sgRNA expression plasmid used for transfection was the same.Fold-activation values were calculated as described in 2A and shown asgrey bars. The calculated sum of mean fold-activation values induced byindividual sgRNAs is shown for each combination as black bars. Asterisksindicate all combinations that were found to be significantly greaterthan the expected sum as determined by an analysis of variance (ANOVA)(p<0.05).

FIG. 3A is a diagram illustrating the positions and orientations of sixsgRNAs targeted to the endogenous human NTF3 gene promoter. Horizontalarrows represent the first 20 nts of the sgRNA complementary to thegenomic DNA sequence with the arrow pointing 5′ to 3′. Grey lineindicates region of potential open chromatin identified from the ENCODEDNaseI hypersensitivity track on the UCSC genome browser with thethicker part of the bar indicating the first transcribed exon. Numberingshown is relative to the transcription start site (+1, right-anglearrow).

FIG. 3B is a bar graph showing activation of NTF3 gene expression bysgRNA-guided dCas9-VP64 in 293 cells. Relative expression of NTF3 mRNA,detected by quantitative RT-PCR and normalized to a GAPDH control(deltaCt×10⁴), is shown for 293 cells co-transfected with the indicatedamounts of dCas9-VP64 and NTF3-targeted sgRNA expression plasmids. Allexperiments were performed in triplicate with error bars representingstandard errors of the mean. Asterisks indicate samples that aresignificantly greater than the off-target gRNA control as determined bya paired, one-sided T-test (P<0.05).

FIG. 3C is a bar graph showing multiplex gRNA expression inducessynergistic activation of NTF3 mRNA expression by dCas9-VP64 protein.Relative expression of NTF3 mRNA, detected by quantitative RT-PCR andnormalized to a GAPDH control (deltaCt×104), is shown for 293 cellsco-transfected with dCas9-VP64 and the indicated combinations ofNTF3-targeted gRNA expression plasmids. Note that in all of theseexperiments the amount of each individual gRNA expression plasmid usedfor transfection was the same. All experiments were performed intriplicate with error bars representing standard errors of the mean. Thecalculated sum of mean fold-activation values induced by individualgRNAs is shown for each combination.

FIG. 4 is an exemplary sequence of an sgRNA expression vector.

FIG. 5 is an exemplary sequence of CMV-T7-Cas9 D10A/H840A-3XFLAG-VP64expression vector.

FIG. 6 is an exemplary sequence of CMV-T7-Cas9 recodedD10A/H840A-3XFLAG-VP64 expression vector.

FIG. 7 is an exemplary sequence of a Cas9-HFD, i.e., a Cas9-activator.An optional 3xFLAG sequence is underlined; the nuclear localizationsignal PKKKRKVS (SEQ ID NO:11) is in lower case; two linkers are inbold; and the VP64 transcriptional activator sequence,DALDDFDLDMLGSDALDDFDLDMLGSDALDDFDLDMLGSDALDDFDLDML (SEQ ID NO:12), isboxed.

FIGS. 8A-8B are exemplary sequences of (8A) dCas9-NLS-3XFLAG-HP1alphaand (8B) dCas9-NLS-3XFLAG-HP1beta. Box=nuclear localization signal;underline=triple flag tag; double underline=HP1alpha hinge andchromoshadow domains.

FIG. 9 is an exemplary sequence of dCas9-TET1.

FIG. 10 is a bar graph showing results obtained with various dCas9-VP64fusion constructs. Of those tested, the optimized dCas9-VP64architecture included an N-terminal NLS (NFN) and an additional NLS (N)or FLAG tag/NLS (NF) placed between dCas9 and VP64. Expression of theVEGFA gene in human HEK293 cells was activated by transcriptionalactivation mediated by RNA-guided dCas9-VP64 fusions. Expressionplasmids encoding variants of dCas9-VP64 were co-transfected with aplasmid that expressed three gRNAs that targeted sites in a regionupstream of the VEGFA start codon (in this experiment, the gRNAs wereexpressed from a single gRNA and processed out by the Csy4endoribonuclease). VEGFA protein expression is measured by ELISA, andthe mean of two replicates is shown with error bars indicating standarderrors of the mean.

FIGS. 11A-B are bar graphs showing the activities of dCas9-VP64activators bearing alternative substitution mutations to catalyticallyinactivate Cas9 function. (11A) Plasmids expressing dCas9-VP64 proteinsbearing various Cas9 inactivating substitutions to residues D10 and H840were each co-transfected into HEK293 cells with either a single gRNA orthree distinctly targeted gRNAs targeting the VEGFA upstream region(blue and red bars, respectively). (11B) Plasmids expressing thesedCas9-VP64 variants were also transfected into a HEK293 cell-line thatstably expresses a single VEGFA-targeted gRNA. VEGFA protein levels weredetermined by ELISA with mean of two replicates and standard errors ofthe mean (error bars) shown.

DETAILED DESCRIPTION

Described herein are fusion proteins of a heterologous functional domain(e.g., a transcriptional activation domain) fused to a catalyticallyinactivated version of the Cas9 protein for the purpose of enablingRNA-guided targeting of these functional domains to specific genomiclocations in cells and living organisms.

The CRISPR/Cas system has evolved in bacteria as a defense mechanism toprotect against invading plasmids and viruses. Short protospacers,derived from foreign nucleic acid, are incorporated into CRISPR loci andsubsequently transcribed and processed into short CRISPR RNAs (crRNAs).These crRNAs, complexed with a second tracrRNA, then use their sequencecomplementarity to the invading nucleic acid to guide Cas9-mediatedcleavage, and consequent destruction of the foreign nucleic acid. In2012, Doudna and colleagues demonstrated that a single guide RNA (sgRNA)composed of a fusion of a crRNA with tracrRNA can mediate recruitment ofCas9 nuclease to specific DNA sequences in vitro (FIG. 1C; Jinek et al.,Science 2012).

More recently, a longer version of the sgRNA has been used to introducetargeted alterations in human cells and zebrafish (FIG. 1B; Mali et al.Science 2013, Hwang and Fu et al., Nat Biotechnol. 2013 March;31(3):227-9). Qi et al. demonstrated that gRNA-mediated recruitment of acatalytically inactive mutant form of Cas9 (referred to as dCas9) couldlead to repression of specific endogenous genes in E. coli as well as ofan EGFP reporter gene in human cells (Qi et al., Cell 152, 1173-1183(2013)). Although this study demonstrated the potential to adaptRNA-guided Cas9 technology for regulation of gene expression, it did nottest or demonstrate whether heterologous functional domains(e.g.—transcriptional activation domains) could be fused to dCas9without disrupting its ability to be recruited to specific genomic sitesby programmable sgRNAs or dual gRNAs (dgRNAs—i.e.—a customized crRNA anda tracrRNA).

As described herein, in addition to guiding Cas9-mediated nucleaseactivity, it is possible to use CRISPR-derived RNAs to targetheterologous functional domains fused to Cas9 (Cas9-HFD) to specificsites in the genome (FIG. 1C). For example, as described herein, it ispossible to use single guide RNAs (sgRNAs) to target Cas9-HFD, e.g.,Cas9-transcriptional activators (hereafter referred to asCas9-activators) to the promoters of specific genes and thereby increaseexpression of the target gene. Thus Cas9-HFD can be localized to sitesin the genome, with target specificity defined by sequencecomplementarity of the guide RNA. The target sequence also includes aPAM sequence (a 2-5 nucleotide sequence specified by the Cas9 proteinwhich is adjacent to the sequence specified by the RNA).

The Cas9-HFD are created by fusing a heterologous functional domain(e.g., a transcriptional activation domain, e.g., from VP64 or NF-κBp65), to the N-terminus or C-terminus of a catalytically inactive Cas9protein.

Cas9

A number of bacteria express Cas9 protein variants. The Cas9 fromStreptococcus pyogenes is presently the most commonly used; some of theother Cas9 proteins have high levels of sequence identity with the S.pyogenes Cas9 and use the same guide RNAs. Others are more diverse, usedifferent gRNAs, and recognize different PAM sequences as well (the 2-5nucleotide sequence specified by the protein which is adjacent to thesequence specified by the RNA). Chylinski et al. classified Cas9proteins from a large group of bacteria (RNA Biology 10:5, 1-12; 2013),and a large number of Cas9 proteins are listed in supplementary FIG. 1and supplementary table 1 thereof, which are incorporated by referenceherein. Additional Cas9 proteins are described in Esvelt et al., NatMethods. 2013 November; 10(11):1116-21 and Fonfara et al., “Phylogeny ofCas9 determines functional exchangeability of dual-RNA and Cas9 amongorthologous type II CRISPR-Cas systems.” Nucleic Acids Res. 2013 Nov.22. [Epub ahead of print] doi:10.1093/nar/gkt1074.

Cas9 molecules of a variety of species can be used in the methods andcompositions described herein. While the S. pyogenes and S. thermophilusCas9 molecules are the subject of much of the disclosure herein, Cas9molecules of, derived from, or based on the Cas9 proteins of otherspecies listed herein can be used as well. In other words, while themuch of the description herein uses S. pyogenes and S. thermophilus Cas9molecules, Cas9 molecules from the other species can replace them. Suchspecies include those set forth in the following table, which wascreated based on supplementary FIG. 1 of Chylinski et al., 2013.

Alternative Cas9 proteins GenBank Acc No. Bacterium 303229466Veillonella atypica ACS-134-V-Col7a 34762592 Fusobacterium nucleatumsubsp. vincentii 374307738 Filifactor alocis ATCC 35896 320528778Solobacterium moorei F0204 291520705 Coprococcus catus GD-7 42525843Treponema denticola ATCC 35405 304438954 Peptoniphilus duerdenii ATCCBAA-1640 224543312 Catenibacterium mitsuokai DSM 15897 24379809Streptococcus mutans UA159 15675041 Streptococcus pyogenes SF37016801805 Listeria innocua Clip11262 116628213 Streptococcus thermophilusLMD-9 323463801 Staphylococcus pseudintermedius ED99 352684361Acidaminococcus intestini RyC-MR95 302336020 Olsenella uli DSM 7084366983953 Oenococcus kitaharae DSM 17330 310286728 Bifidobacteriumbifidum S17 258509199 Lactobacillus rhamnosus GG 300361537 Lactobacillusgasseri JV-V03 169823755 Finegoldia magna ATCC 29328 47458868 Mycoplasmamobile 163K 284931710 Mycoplasma gallisepticum str. F 363542550Mycoplasma ovipneumoniae SC01 384393286 Mycoplasma canis PG 14 71894592Mycoplasma synoviae 53 238924075 Eubacterium rectale ATCC 33656116627542 Streptococcus thermophilus LMD-9 315149830 Enterococcusfaecalis TX0012 315659848 Staphylococcus lugdunensis M23590 160915782Eubacterium dolichum DSM 3991 336393381 Lactobacillus coryniformissubsp. torquens 310780384 Ilyobacter polytropus DSM 2926 325677756Ruminococcus albus 8 187736489 Akkermansia muciniphila ATCC BAA-835117929158 Acidothermus cellulolyticus 11B 189440764 Bifidobacteriumlongum DJO10A 283456135 Bifidobacterium dentium Bd1 38232678Corynebacterium diphtheriae NCTC 13129 187250660 Elusimicrobium minutumPei191 319957206 Nitratifractor salsuginis DSM 16511 325972003Sphaerochaeta globus str. Buddy 261414553 Fibrobacter succinogenessubsp. succinogenes 60683389 Bacteroides fragilis NCTC 9343 256819408Capnocytophaga ochracea DSM 7271 90425961 Rhodopseudomonas palustrisBisB18 373501184 Prevotella micans F0438 294674019 Prevotella ruminicola23 365959402 Flavobacterium columnare ATCC 49512 312879015 Aminomonaspaucivorans DSM 12260 83591793 Rhodospirillum rubrum ATCC 11170294086111 Candidatus Puniceispirillum marinum IMCC1322 121608211Verminephrobacter eiseniae EF01-2 344171927 Ralstonia syzygii R24159042956 Dinoroseobacter shibae DFL 12 288957741 Azospirillum sp- B51092109262 Nitrobacter hamburgensis X14 148255343 Bradyrhizobium sp- BTAi134557790 Wolinella succinogenes DSM 1740 218563121 Campylobacter jejunisubsp. jejuni 291276265 Helicobacter mustelae 12198 229113166 Bacilluscereus Rock1-15 222109285 Acidovorax ebreus TPSY 189485225 unculturedTermite group 1 182624245 Clostridium perfringens D str. 220930482Clostridium cellulolyticum H10 154250555 Parvibaculum lavamentivoransDS-1 257413184 Roseburia intestinalis L1-82 218767588 Neisseriameningitidis Z2491 15602992 Pasteurella multocida subsp. multocida319941583 Sutterella wadsworthensis 3 1 254447899 gamma proteobacteriumHTCC5015 54296138 Legionella pneumophila str. Paris 331001027Parasutterella excrementihominis YIT 11859 34557932 Wolinellasuccinogenes DSM 1740 118497352 Francisella novicida U112The constructs and methods described herein can include the use of anyof those Cas9 proteins, and their corresponding guide RNAs or otherguide RNAs that are compatible. The Cas9 from Streptococcus thermophilusLMD-9 CRISPR1 system has been shown to function in human cells in Conget al (Science 339, 819 (2013)). Additionally, Jinek et al. showed invitro that Cas9 orthologs from S. thermophilus and L. innocua, (but notfrom N. meningitidis or C. jejuni, which likely use a different guideRNA), can be guided by a dual S. pyogenes gRNA to cleave target plasmidDNA, albeit with slightly decreased efficiency.

In some embodiments, the present system utilizes the Cas9 protein fromS. pyogenes, either as encoded in bacteria or codon-optimized forexpression in mammalian cells, containing mutations at D10, E762, H983,or D986 and H840 or N863, e.g., D10A/D10N and H840A/H840N/H840Y, torender the nuclease portion of the protein catalytically inactive;substitutions at these positions could be alanine (as they are inNishimasu al., Cell 156, 935-949 (2014)) or they could be otherresidues, e.g., glutamine, asparagine, tyrosine, serine, or aspartate,e.g., E762Q, H983N, H983Y, D986N, N863D, N863S, or N863H (FIG. 1C). Thesequence of the catalytically inactive S. pyogenes Cas9 that can be usedin the methods and compositions described herein is as follows; theexemplary mutations of D10A and H840A are in bold and underlined.

(SEQ ID NO: 13)        10         20         30         40         50         60MDKKYSIGL A  IGTNSVGWAV ITDEYKVPSK KFKVLGNTDR HSIKKNLIGA LLFDSGETAE        70         80         90        100        110        120ATRLKRTARR RYTRRKNRIC YLQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG       130        140        150        160        170        180NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH MIKFRGHFLI EGDLNPDNSD       190        200        210        220        230        240VDKLFIQLVQ TYNQLFEENP INASGVDAKA ILSARLSKSR RLENLIAQLP GEKKNGLFGN       250        260        270        280        290        300LIALSLGLTP NFKSNFDLAE DAKLQLSKDT YDDDLDNLLA QIGDQYADLF LAAKNLSDAI       310        320        330        340        350        360LLSDILRVNT EITKAPLSAS MIKRYDEHHQ DLTLLKALVR QQLPEKYKEI FFDQSKNGYA       370        380        390        400        410        420GYIDGGASQE EFYKFIKPIL EKMDGTEELL VKLNREDLLR KQRTFDNGSI PHQIHLGELH       430        440        450        460        470        480AILRRQEDFY PFLKDNREKI EKILTFRIPY YVGPLARGNS RFAWMTRKSE ETITPWNFEE       490        500        510        520        530        540VVDKGASAQS FIERMTNFDK NLPNEKVLPK HSLLYEYFTV YNELTKVKYV TEGMRKPAFL       550        560        570        580        590        600SGEQKKAIVD LLFKTNRKVT VKQLKEDYFK KIECFDSVEI SGVEDRFNAS LGTYHDLLKI       610        620        630        640        650        660IKDKDFLDNE ENEDILEDIV LTLTLFEDRE MIEERLKTYA HLFDDKVMKQ LKRRRYTGWG       670        680        690        700        710        720RLSRKLINGI RDKQSGKTIL DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL       730        740        750        760        770        780HEHIANLAGS PAIKKGILQT VKVVDELVKV MGRHKPENIV IEMARENQTT QKGQKNSRER       790        800        810        820        830        840MKRIEEGIKE LGSQILKEHP VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVD A       850        860        870        880        890        900IVPQSFLKDD SIDNKVLTRS DKNRGKSDNV PSEEVVKKMK NYWRQLLNAK LITQRKFDNL       910        920        930        940        950        960TKAERGGLSE LDKAGFIKRQ LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS       970        980        990       1000       1010       1020KLVSDFRKDF QFYKVREINN YHHAHDAYLN AVVGTALIKK YPKLESEFVY GDYKVYDVRK      1030       1040       1050       1060       1070       1080MIAKSEQEIG KATAKYFFYS NIMNFFKTEI TLANGEIRKR PLIETNGETG EIVWDKGRDF      1090       1100       1110       1120       1130       1140ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI ARKKDWDPKK YGGFDSPTVA      1150       1160       1170       1180       1190       1200YSVLVVAKVE KGKSKKLKSV KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK      1210       1220       1230       1240       1250       1260YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS HYEKLKGSPE DNEQKQLFVE      1270       1280       1290       1300       1310       1320QHKHYLDEII EQISEFSKRV ILADANLDKV LSAYNKHRDK PIREQAENII HLFTLTNLGA      1330       1340       1350       1360PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGD

In some embodiments, the Cas9 nuclease used herein is at least about 50%identical to the sequence of S. pyogenes Cas9, i.e., at least 50%identical to SEQ ID NO:13. In some embodiments, the nucleotide sequencesare about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100%identical to SEQ ID NO:13.

In some embodiments, the catalytically inactive Cas9 used herein is atleast about 50% identical to the sequence of the catalytically inactiveS. pyogenes Cas9, i.e., at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%,90%, 95%, 99% or 100% identical to SEQ ID NO:13, wherein the mutationsat D10 and H840, e.g., D10A/D10N and H840A/H840N/H840Y are maintained.

In some embodiments, any differences from SEQ ID NO:13 are innon-conserved regions, as identified by sequence alignment of sequencesset forth in Chylinski et al., RNA Biology 10:5, 1-12; 2013 (e.g., insupplementary FIG. 1 and supplementary table 1 thereof); Esvelt et al.,Nat Methods. 2013 November; 10(11):1116-21 and Fonfara et al., Nucl.Acids Res. (2014) 42 (4): 2577-2590. [Epub ahead of print 2013 Nov. 22]doi:10.1093/nar/gkt1074, and wherein the mutations at D10 and H840,e.g., D10A/D10N and H840A/H840N/H840Y are maintained.

To determine the percent identity of two sequences, the sequences arealigned for optimal comparison purposes (gaps are introduced in one orboth of a first and a second amino acid or nucleic acid sequence asrequired for optimal alignment, and non-homologous sequences can bedisregarded for comparison purposes). The length of a reference sequencealigned for comparison purposes is at least 50% (in some embodiments,about 50%, 55%, 60%, 65%, 70%, 75%, 85%, 90%, 95%, or 100% of the lengthof the reference sequence) is aligned. The nucleotides or residues atcorresponding positions are then compared. When a position in the firstsequence is occupied by the same nucleotide or residue as thecorresponding position in the second sequence, then the molecules areidentical at that position. The percent identity between the twosequences is a function of the number of identical positions shared bythe sequences, taking into account the number of gaps, and the length ofeach gap, which need to be introduced for optimal alignment of the twosequences.

The comparison of sequences and determination of percent identitybetween two sequences can be accomplished using a mathematicalalgorithm. For purposes of the present application, the percent identitybetween two amino acid sequences is determined using the Needleman andWunsch ((1970) J. Mol. Biol. 48:444-453) algorithm which has beenincorporated into the GAP program in the GCG software package, using aBlossum 62 scoring matrix with a gap penalty of 12, a gap extend penaltyof 4, and a frameshift gap penalty of 5.

Heterologous Functional Domains

The transcriptional activation domains can be fused on the N or Cterminus of the Cas9. In addition, although the present descriptionexemplifies transcriptional activation domains, other heterologousfunctional domains (e.g., transcriptional repressors (e.g., KRAB, ERD,SID, and others, e.g., amino acids 473-530 of the ets2 repressor factor(ERF) repressor domain (ERD), amino acids 1-97 of the KRAB domain ofKOX1, or amino acids 1-36 of the Mad mSIN3 interaction domain (SID); seeBeerli et al., PNAS USA 95:14628-14633 (1998)) or silencers such asHeterochromatin Protein 1 (HP1, also known as swi6), e.g., HP1α or HP1β;proteins or peptides that could recruit long non-coding RNAs (lncRNAs)fused to a fixed RNA binding sequence such as those bound by the MS2coat protein, endoribonuclease Csy4, or the lambda N protein; enzymesthat modify the methylation state of DNA (e.g., DNA methyltransferase(DNMT) or TET proteins); or enzymes that modify histone subunits (e.g.,histone acetyltransferases (HAT), histone deacetylases (HDAC), histonemethyltransferases (e.g., for methylation of lysine or arginineresidues) or histone demethylases (e.g., for demethylation of lysine orarginine residues)) as are known in the art can also be used. A numberof sequences for such domains are known in the art, e.g., a domain thatcatalyzes hydroxylation of methylated cytosines in DNA. Exemplaryproteins include the Ten-Eleven-Translocation (TET)1-3 family, enzymesthat converts 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC)in DNA.

Sequences for human TET1-3 are known in the art and are shown in thefollowing table:

GenBank Accession Nos. Gene Amino Acid Nucleic Acid TET1 NP_085128.2NM_030625.2 TET2* NP_001120680.1 (var 1) NM_001127208.2 NP_060098.3(var2) NM_017628.4 TET3 NP_659430.1 NM_144993.1 *Variant (1) representsthe longer transcript and encodes the longer isoform (a). Variant (2)differs in the 5′ UTR and in the 3′ UTR and coding sequence compared tovariant 1. The resulting isoform (b) is shorter and has a distinctC-terminus compared to isoform a.

In some embodiments, all or part of the full-length sequence of thecatalytic domain can be included, e.g., a catalytic module comprisingthe cysteine-rich extension and the 2OGFeDO domain encoded by 7 highlyconserved exons, e.g., the Tet1 catalytic domain comprising amino acids1580-2052, Tet2 comprising amino acids 1290-1905 and Tet3 comprisingamino acids 966-1678. See, e.g., FIG. 1 of Iyer et al., Cell Cycle. 2009Jun. 1; 8(11):1698-710. Epub 2009 Jun. 27, for an alignment illustratingthe key catalytic residues in all three Tet proteins, and thesupplementary materials thereof (available at ftp siteftp.ncbi.nih.gov/pub/aravind/DONS/supplementary material DONS.html) forfull length sequences (see, e.g., seq 2c); in some embodiments, thesequence includes amino acids 1418-2136 of Tet1 or the correspondingregion in Tet2/3.

Other catalytic modules can be from the proteins identified in Iyer etal., 2009.

In some embodiments, the heterologous functional domain is a biologicaltether, and comprises all or part of (e.g., DNA binding domain from) theMS2 coat protein, endoribonuclease Csy4, or the lambda N protein. Theseproteins can be used to recruit RNA molecules containing a specificstem-loop structure to a locale specified by the dCas9 gRNA targetingsequences. For example, a dCas9 fused to MS2 coat protein,endoribonuclease Csy4, or lambda N can be used to recruit a longnon-coding RNA (lncRNA) such as XIST or HOTAIR; see, e.g., Keryer-Bibenset al., Biol. Cell 100:125-138 (2008), that is linked to the Csy4, MS2or lambda N binding sequence. Alternatively, the Csy4, MS2 or lambda Nprotein binding sequence can be linked to another protein, e.g., asdescribed in Keryer-Bibens et al., supra, and the protein can betargeted to the dCas9 binding site using the methods and compositionsdescribed herein. In some embodiments, the Csy4 is catalyticallyinactive.

In some embodiments, the fusion proteins include a linker between thedCas9 and the heterologous functional domains. Linkers that can be usedin these fusion proteins (or between fusion proteins in a concatenatedstructure) can include any sequence that does not interfere with thefunction of the fusion proteins. In preferred embodiments, the linkersare short, e.g., 2-20 amino acids, and are typically flexible (i.e.,comprising amino acids with a high degree of freedom such as glycine,alanine, and serine). In some embodiments, the linker comprises one ormore units consisting of GGGS (SEQ ID NO:14) or GGGGS (SEQ ID NO:15),e.g., two, three, four, or more repeats of the GGGS (SEQ ID NO:14) orGGGGS (SEQ ID NO:15) unit. Other linker sequences can also be used.

Methods of Use

The described Cas9-HFD system is a useful and versatile tool formodifying the expression of endogenous genes. Current methods forachieving this require the generation of novel engineered DNA-bindingproteins (such as engineered zinc finger or transcription activator-likeeffector DNA binding domains) for each site to be targeted. Becausethese methods demand expression of a large protein specificallyengineered to bind each target site, they are limited in their capacityfor multiplexing. Cas9-HFD, however, require expression of only a singleCas9-HFD protein, which can be targeted to multiple sites in the genomeby expression of multiple short gRNAs. This system could thereforeeasily be used to simultaneously induce expression of a large number ofgenes or to recruit multiple Cas9-HFDs to a single gene, promoter, orenhancer. This capability will have broad utility, e.g., for basicbiological research, where it can be used to study gene function and tomanipulate the expression of multiple genes in a single pathway, and insynthetic biology, where it will enable researchers to create circuitsin cell that are responsive to multiple input signals. The relative easewith which this technology can be implemented and adapted tomultiplexing will make it a broadly useful technology with manywide-ranging applications.

The methods described herein include contacting cells with a nucleicacid encoding the Cas9-HFD described herein, and nucleic acids encodingone or more guide RNAs directed to a selected gene, to thereby modulateexpression of that gene.

Guide RNAs (gRNAs)

Guide RNAs generally speaking come in two different systems: System 1,which uses separate crRNA and tracrRNAs that function together to guidecleavage by Cas9, and System 2, which uses a chimeric crRNA-tracrRNAhybrid that combines the two separate guide RNAs in a single system(referred to as a single guide RNA or sgRNA, see also Jinek et al.,Science 2012; 337:816-821). The tracrRNA can be variably truncated and arange of lengths has been shown to function in both the separate system(system 1) and the chimeric gRNA system (system 2). For example, in someembodiments, tracrRNA may be truncated from its 3′ end by at least 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts. In someembodiments, the tracrRNA molecule may be truncated from its 5′ end byat least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts.Alternatively, the tracrRNA molecule may be truncated from both the 5′and 3′ end, e.g., by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15 or 20nts on the 5′ end and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20,25, 30, 35 or 40 nts on the 3′ end. See, e.g., Jinek et al., Science2012; 337:816-821; Mali et al., Science. 2013 Feb. 15; 339(6121):823-6;Cong et al., Science. 2013 Feb. 15; 339(6121):819-23; and Hwang and Fuet al., Nat Biotechnol. 2013 March; 31(3):227-9; Jinek et al., Elife 2,e00471 (2013)). For System 2, generally the longer length chimeric gRNAshave shown greater on-target activity but the relative specificities ofthe various length gRNAs currently remain undefined and therefore it maybe desirable in certain instances to use shorter gRNAs. In someembodiments, the gRNAs are complementary to a region that is withinabout 100-800 bp upstream of the transcription start site, e.g., iswithin about 500 bp upstream of the transcription start site, includesthe transcription start site, or within about 100-800 bp, e.g., withinabout 500 bp, downstream of the transcription start site. In someembodiments, vectors (e.g., plasmids) encoding more than one gRNA areused, e.g., plasmids encoding, 2, 3, 4, 5, or more gRNAs directed todifferent sites in the same region of the target gene.

Cas9 nuclease can be guided to specific 17-20 nt genomic targets bearingan additional proximal protospacer adjacent motif (PAM), e.g., ofsequence NGG using a guide RNA, e.g., a single gRNA or a tracrRNA/crRNA,bearing 17-20 nts at its 5′ end that are complementary to thecomplementary strand of the genomic DNA target site. Thus, the presentmethods can include the use of a single guide RNA comprising a crRNAfused to a normally trans-encoded tracrRNA, e.g., a single Cas9 guideRNA as described in Mali et al., Science 2013 Feb. 15; 339(6121):823-6,with a sequence at the 5′ end that is complementary to the targetsequence, e.g., of 25-17, optionally 20 or fewer nucleotides (nts),e.g., 20, 19, 18, or 17 nts, preferably 17 or 18 nts, of thecomplementary strand to a target sequence immediately 5′ of aprotospacer adjacent motif (PAM), e.g., NGG, NAG; or NNGG In someembodiments, the single Cas9 guide RNA consists of the sequence:

(SEQ ID NO: 1) (X₁₇₋₂₀)GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCG(X_(N)); (SEQ ID NO: 2)(X₁₇₋₂₀)GUUUUAGAGCUAUGCUGAAAAGCAUAGCAAGUUAAAAUAAGGC UAGUCCGUUAUC(X_(N));(SEQ ID NO: 3) (X₁₇₋₂₀)GUUUUAGAGCUAUGCUGUUUUGGAAACAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUC(X_(N)); (SEQ ID NO: 4)(X₁₇₋₂₀)GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC(X_(N)), (SEQ ID NO: 5)(X₁₇₋₂₀)GUUUAAGAGCUAGAAAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC; (SEQ ID NO: 6)(X₁₇₋₂₀)GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC; or (SEQ ID NO: 7)(X₁₇₋₂₀)GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC;wherein X₁₇₋₂₀ is the nucleotide sequence complementary to 17-20consecutive nucleotides of the target sequence. DNAs encoding the singleguide RNAs have been described previously in the literature (Jinek etal., Science. 337(6096):816-21 (2012) and Jinek et al., Elife. 2:e00471(2013)).

The guide RNAs can include X_(N) which can be any sequence, wherein N(in the RNA) can be 0-200, e.g., 0-100, 0-50, or 0-20, that does notinterfere with the binding of the ribonucleic acid to Cas9.

In some embodiments, the guide RNA includes one or more Adenine (A) orUracil (U) nucleotides on the 3′ end. In some embodiments the RNAincludes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU,UUUUU, UUUUUU, UUUUUUU, UUUUUUUU) at the 3′ end of the molecule, as aresult of the optional presence of one or more Ts used as a terminationsignal to terminate RNA PolIII transcription.

Although some of the examples described herein utilize a single gRNA,the methods can also be used with dual gRNAs (e.g., the crRNA andtracrRNA found in naturally occurring systems). In this case, a singletracrRNA would be used in conjunction with multiple different crRNAsexpressed using the present system, e.g., the following:

(X₁₇₋₂₀)GUUUUAGAGCUA (SEQ ID NO:102); (X₁₇₋₂₀) GUUUUAGAGCUAUGCUGUUUUG(SEQ ID NO:103); or

(X₁₇₋₂₀)GUUUUAGAGCUAUGCU (SEQ ID NO:104); and a tracrRNA sequence. Inthis case, the crRNA is used as the guide RNA in the methods andmolecules described herein, and the tracrRNA can be expressed from thesame or a different DNA molecule. In some embodiments, the methodsinclude contacting the cell with a tracrRNA comprising or consisting ofthe sequenceGGAACCAUUCAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC (SEQ ID NO:8) or an active portion thereof(an active portion is one that retains the ability to form complexeswith Cas9 or dCas9). In some embodiments, the tracrRNA molecule may betruncated from its 3′ end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15,20, 25, 30, 35 or 40 nts. In another embodiment, the tracrRNA moleculemay be truncated from its 5′ end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 15, 20, 25, 30, 35 or 40 nts. Alternatively, the tracrRNA moleculemay be truncated from both the 5′ and 3′ end, e.g., by at least 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 15 or 20 nts on the 5′ end and at least 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts on the 3′ end.Exemplary tracrRNA sequences in addition to SEQ ID NO:8 include thefollowing:UAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCG AGUCGGUGC (SEQ IDNO:105) or an active portion thereof; orAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGC ACCGAGUCGGUGC (SEQID NO:106) or an active portion thereof.

In some embodiments when (X₁₇₋₂₀)GUUUUAGAGCUAUGCUGUUUUG (SEQ ID NO:102)is used as a crRNA, the following tracrRNA is used:

GGAACCAUUCAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC (SEQ ID NO:8) or an active portion thereof.

In some embodiments when (X₁₇₋₂₀)GUUUUAGAGCUA (SEQ ID NO:102) is used asa crRNA, the following tracrRNA is used:

UAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCG AGUCGGUGC (SEQ IDNO:105) or an active portion thereof.

In some embodiments when (X₁₇₋₂₀) GUUUUAGAGCUAUGCU (SEQ ID NO:104) isused as a crRNA, the following tracrRNA is used:

AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGC ACCGAGUCGGUGC (SEQID NO:106) or an active portion thereof.

In some embodiments, the gRNA is targeted to a site that is at leastthree or more mismatches different from any sequence in the rest of thegenome in order to minimize off-target effects.

Modified RNA oligonucleotides such as locked nucleic acids (LNAs) havebeen demonstrated to increase the specificity of RNA-DNA hybridizationby locking the modified oligonucleotides in a more favorable (stable)conformation. For example, 2′-O-methyl RNA is a modified base wherethere is an additional covalent linkage between the 2′ oxygen and 4′carbon which when incorporated into oligonucleotides can improve overallthermal stability and selectivity (Formula I).

Thus in some embodiments, the tru-gRNAs disclosed herein may compriseone or more modified RNA oligonucleotides. For example, the truncatedguide RNAs molecules described herein can have one, some or all of theregion of the guideRNA complementary to the target sequence aremodified, e.g., locked (2′-O-4′-C methylene bridge), 5′-methylcytidine,2′-O-methyl-pseudouridine, or in which the ribose phosphate backbone hasbeen replaced by a polyamide chain (peptide nucleic acid), e.g., asynthetic ribonucleic acid.

In other embodiments, one, some or all of the nucleotides of thetru-gRNA sequence may be modified, e.g., locked (2′-O-4′-C methylenebridge), 5′-methylcytidine, 2′-O-methyl-pseudouridine, or in which theribose phosphate backbone has been replaced by a polyamide chain(peptide nucleic acid), e.g., a synthetic ribonucleic acid.

In some embodiments, the single guide RNAs and/or crRNAs and/ortracrRNAs can include one or more Adenine (A) or Uracil (U) nucleotideson the 3′ end.

Existing Cas9-based RGNs use gRNA-DNA heteroduplex formation to guidetargeting to genomic sites of interest. However, RNA-DNA heteroduplexescan form a more promiscuous range of structures than their DNA-DNAcounterparts. In effect, DNA-DNA duplexes are more sensitive tomismatches, suggesting that a DNA-guided nuclease may not bind asreadily to off-target sequences, making them comparatively more specificthan RNA-guided nucleases. Thus, the guide RNAs usable in the methodsdescribed herein can be hybrids, i.e., wherein one or moredeoxyribonucleotides, e.g., a short DNA oligonucleotide, replaces all orpart of the gRNA, e.g., all or part of the complementarity region of agRNA. This DNA-based molecule could replace either all or part of thegRNA in a single gRNA system or alternatively might replace all of partof the crRNA and/or tracrRNA in a dual crRNA/tracrRNA system. Such asystem that incorporates DNA into the complementarity region should morereliably target the intended genomic DNA sequences due to the generalintolerance of DNA-DNA duplexes to mismatching compared to RNA-DNAduplexes. Methods for making such duplexes are known in the art, See,e.g., Barker et al., BMC Genomics. 2005 Apr. 22; 6:57; and Sugimoto etal., Biochemistry. 2000 Sep. 19; 39(37):11270-81.

In addition, in a system that uses separate crRNA and tracrRNA, one orboth can be synthetic and include one or more modified (e.g., locked)nucleotides or deoxyribonucleotides.

In a cellular context, complexes of Cas9 with these synthetic gRNAscould be used to improve the genome-wide specificity of the CRISPR/Cas9nuclease system.

The methods described can include expressing in a cell, or contactingthe cell with, a Cas9 gRNA plus a fusion protein as described herein.

Expression Systems

In order to use the fusion proteins and guide RNAs described herein, itmay be desirable to express them from a nucleic acid that encodes them.This can be performed in a variety of ways. For example, a nucleic acidencoding a guide RNA or fusion protein can be cloned into anintermediate vector for transformation into prokaryotic or eukaryoticcells for replication and/or expression. Intermediate vectors aretypically prokaryote vectors, e.g., plasmids, or shuttle vectors, orinsect vectors, for storage or manipulation of the nucleic acid encodingthe fusion protein or for production of the fusion protein. The nucleicacid encoding the guide RNA or fusion protein can also be cloned into anexpression vector, for administration to a plant cell, animal cell,preferably a mammalian cell or a human cell, fungal cell, bacterialcell, or protozoan cell.

To obtain expression, a sequence encoding a guide RNA or fusion proteinis typically subcloned into an expression vector that contains apromoter to direct transcription. Suitable bacterial and eukaryoticpromoters are well known in the art and described, e.g., in Sambrook etal., Molecular Cloning, A Laboratory Manual (3d ed. 2001); Kriegler,Gene Transfer and Expression: A Laboratory Manual (1990); and CurrentProtocols in Molecular Biology (Ausubel et al., eds., 2010). Bacterialexpression systems for expressing the engineered protein are availablein, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al., 1983,Gene 22:229-235). Kits for such expression systems are commerciallyavailable. Eukaryotic expression systems for mammalian cells, yeast, andinsect cells are well known in the art and are also commerciallyavailable.

The promoter used to direct expression of the nucleic acid depends onthe particular application. For example, a strong constitutive promoteris typically used for expression and purification of fusion proteins. Incontrast, when the fusion protein is to be administered in vivo for generegulation, either a constitutive or an inducible promoter can be used,depending on the particular use of the fusion protein. In addition, apreferred promoter for administration of the fusion protein can be aweak promoter, such as HSV TK or a promoter having similar activity. Thepromoter can also include elements that are responsive totransactivation, e.g., hypoxia response elements, Gal4 responseelements, lac repressor response element, and small molecule controlsystems such as tetracycline-regulated systems and the RU-486 system(see, e.g., Gossen & Bujard, 1992, Proc. Natl. Acad. Sci. USA, 89:5547;Oligino et al., 1998, Gene Ther., 5:491-496; Wang et al., 1997, GeneTher., 4:432-441; Neering et al., 1996, Blood, 88:1147-55; and Rendahlet al., 1998, Nat. Biotechnol., 16:757-761).

In addition to the promoter, the expression vector typically contains atranscription unit or expression cassette that contains all theadditional elements required for the expression of the nucleic acid inhost cells, either prokaryotic or eukaryotic. A typical expressioncassette thus contains a promoter operably linked, e.g., to the nucleicacid sequence encoding the fusion protein, and any signals required,e.g., for efficient polyadenylation of the transcript, transcriptionaltermination, ribosome binding sites, or translation termination.Additional elements of the cassette may include, e.g., enhancers, andheterologous spliced intronic signals.

The particular expression vector used to transport the geneticinformation into the cell is selected with regard to the intended use ofthe fusion protein, e.g., expression in plants, animals, bacteria,fungus, protozoa, etc. Standard bacterial expression vectors includeplasmids such as pBR322 based plasmids, pSKF, pET23D, and commerciallyavailable tag-fusion expression systems such as GST and LacZ. Apreferred tag-fusion protein is the maltose binding protein (MBP). Suchtag-fusion proteins can be used for purification of the engineered TALErepeat protein. Epitope tags can also be added to recombinant proteinsto provide convenient methods of isolation, for monitoring expression,and for monitoring cellular and subcellular localization, e.g., c-myc orFLAG

Expression vectors containing regulatory elements from eukaryoticviruses are often used in eukaryotic expression vectors, e.g., SV40vectors, papilloma virus vectors, and vectors derived from Epstein-Barrvirus. Other exemplary eukaryotic vectors include pMSG, pAV009/A+,pMTO10/A+, pMAMneo-5, baculovirus pDSVE, and any other vector allowingexpression of proteins under the direction of the SV40 early promoter,SV40 late promoter, metallothionein promoter, murine mammary tumor viruspromoter, Rous sarcoma virus promoter, polyhedrin promoter, or otherpromoters shown effective for expression in eukaryotic cells.

The vectors for expressing the guide RNAs can include RNA Pol IIIpromoters to drive expression of the guide RNAs, e.g., the H1, U6 or 7SKpromoters. These human promoters allow for expression of gRNAs inmammalian cells following plasmid transfection. Alternatively, a T7promoter may be used, e.g., for in vitro transcription, and the RNA canbe transcribed in vitro and purified. Vectors suitable for theexpression of short RNAs, e.g., siRNAs, shRNAs, or other small RNAs, canbe used.

Some expression systems have markers for selection of stably transfectedcell lines such as thymidine kinase, hygromycin B phosphotransferase,and dihydrofolate reductase. High yield expression systems are alsosuitable, such as using a baculovirus vector in insect cells, with thefusion protein encoding sequence under the direction of the polyhedrinpromoter or other strong baculovirus promoters.

The elements that are typically included in expression vectors alsoinclude a replicon that functions in E. coli, a gene encoding antibioticresistance to permit selection of bacteria that harbor recombinantplasmids, and unique restriction sites in nonessential regions of theplasmid to allow insertion of recombinant sequences.

Standard transfection methods are used to produce bacterial, mammalian,yeast or insect cell lines that express large quantities of protein,which are then purified using standard techniques (see, e.g., Colley etal., 1989, J. Biol. Chem., 264:17619-22; Guide to Protein Purification,in Methods in Enzymology, vol. 182 (Deutscher, ed., 1990)).Transformation of eukaryotic and prokaryotic cells are performedaccording to standard techniques (see, e.g., Morrison, 1977, J.Bacteriol. 132:349-351; Clark-Curtiss & Curtiss, Methods in Enzymology101:347-362 (Wu et al., eds, 1983).

Any of the known procedures for introducing foreign nucleotide sequencesinto host cells may be used. These include the use of calcium phosphatetransfection, polybrene, protoplast fusion, electroporation,nucleofection, liposomes, microinjection, naked DNA, plasmid vectors,viral vectors, both episomal and integrative, and any of the otherwell-known methods for introducing cloned genomic DNA, cDNA, syntheticDNA or other foreign genetic material into a host cell (see, e.g.,Sambrook et al., supra). It is only necessary that the particulargenetic engineering procedure used be capable of successfullyintroducing at least one gene into the host cell capable of expressingthe protein of choice.

In some embodiments, the fusion protein includes a nuclear localizationdomain which provides for the protein to be translocated to the nucleus.Several nuclear localization sequences (NLS) are known, and any suitableNLS can be used. For example, many NLSs have a plurality of basic aminoacids, referred to as a bipartite basic repeats (reviewed inGarcia-Bustos et al, 1991, Biochim. Biophys. Acta, 1071:83-101). An NLScontaining bipartite basic repeats can be placed in any portion ofchimeric protein and results in the chimeric protein being localizedinside the nucleus. In preferred embodiments a nuclear localizationdomain is incorporated into the final fusion protein, as the ultimatefunctions of the fusion proteins described herein will typically requirethe proteins to be localized in the nucleus. However, it may not benecessary to add a separate nuclear localization domain in cases wherethe DBD domain itself, or another functional domain within the finalchimeric protein, has intrinsic nuclear translocation function.

The present invention includes the vectors and cells comprising thevectors.

EXAMPLES

The invention is further described in the following examples, which donot limit the scope of the invention described in the claims.

Example 1. Engineering CRISPR/Cas Activator System

It was hypothesized that RNA-guided transcriptional activators could becreated by fusing the strong synthetic VP64 activation domain (Beerli etal., Proc Natl Acad Sci USA 95, 14628-14633 (1998)) to thecarboxy-terminus of the catalytically inactivated dCas9 protein (FIG.1D).

To express guide RNAs (gRNAs) in human cells, a vector was engineeredthat would express the full length chimeric gRNA (a fusion of crRNA andtracrRNA originally described by Jinek et al. (Science 2012)) driven bya U6 promoter. Construction of the gRNA expression plasmids wasperformed as follows. Pairs of DNA oligonucleotides encoding thevariable 20 nt gRNA targeting sequences were annealed together togenerate short double-strand DNA fragments with 4 bp overhangs (Table1).

TABLE 1 VEGFA and NTF3 gene target sites and associatedoligonucleotides used to construct gRNA expression plasmids. gRNATarget Site (including PAM) SEQ ID NO: V1 GTGTGCAGACGGCAGTCACTAGG 16. V2GAGCAGCGTCTTCGAGAGTGAGG 17. V3 GGTGAGTGAGTGTGTGCGTGTGG 18. V4GTTGGAGCGGGGAGAAGGCCAGG 19. V5 GGGTGGGGGGAGTTTGCTCCTGG 20. V6GGCTTTGGAAAGGGGGTGGGGGG 21. V7 GGGGCGGGGTCCCGGCGGGGCGG 22. V8GCTCGGAGGTCGTGGCGCTGGGG 23. V9 GACTCACCGGCCAGGGCGCTCGG 24. V10GGCGCAGCGGTTAGGTGGACCGG 25. V11 GGCGCATGGCTCCGCCCCGCCGG 26. V12GCCACGACCTCCGAGCTACCCGG 27. V13 GCGGCGTGAGCCCTCCCCCTTGG 28. V14GGAGGCGGGGTGGAGGGGGTCGG 29. V15 GGGCTCACGCCGCGCTCCGGCGG 30. V16GACCCCCTCCACCCCGCCTCCGG 31. Ni GAGCGCGGAGCCATCTGGCCGGG 32. N2GCGCGGCGCGGAAGGGGTTAAGG 33. N3 GCGGCGCGGCGCGGGCCGGCGGG 34. N4GCCGCGCCGCCCTCCCCCGCCGG 35. N5 GCGGTTATAACCAGCCAACCCGG 36. N6GTGCGCGGAGCTGTTCGGAAGGG 37. gRNA top oligo SEQ ID NO: V1ACACCGTGTGCAGACGGCAGTCACTG 38. V2 ACACCGAGCAGCGTCTTCGAGAGTGG 39. V3ACACCGGTGAGTGAGTGTGTGCGTGG 40. V4 ACACCGTTGGAGCGGGGAGAAGGCCG 41. V5ACACCGGGTGGGGGGAGTTTGCTCCG 42. V6 ACACCGGCTTTGGAAAGGGGGTGGGG 43. V7ACACCGGGGCGGGGTCCCGGCGGGGG 44. V8 ACACCGCTCGGAGGTCGTGGCGCTGG 45. V9ACACCGACTCACCGGCCAGGGCGCTG 46. V10 ACACCGGCGCAGCGGTTAGGTGGACG 47. V11ACACCGGCGCATGGCTCCGCCCCGCG 48. V12 ACACCGCCACGACCTCCGAGCTACCG 49. V13ACACCGCGGCGTGAGCCCTCCCCCTG 50. V14 ACACCGGAGGCGGGGTGGAGGGGGTG 51. V15ACACCGGGCTCACGCCGCGCTCCGGG 52. V16 ACACCGACCCCCTCCACCCCGCCTCG 53. NiACACCGAGCGCGGAGCCATCTGGCCG 54. N2 ACACCGCGCGGCGCGGAAGGGGTTAG 55. N3ACACCGCGGCGCGGCGCGGGCCGGCG 56. N4 ACACCGCCGCGCCGCCCTCCCCCGCG 57. N5ACACCGCGGTTATAACCAGCCAACCG 58. N6 ACACCGTGCGCGGAGCTGTTCGGAAG 59. gRNAbottom oligo SEQ ID NO: V1 AAAACAGTGACTGCCGTCTGCACACG 60. V2AAAACCACTCTCGAAGACGCTGCTCG 61. V3 AAAACCACGCACACACTCACTCACCG 62. V4AAAACGGCCTTCTCCCCGCTCCAACG 63. V5 AAAACGGAGCAAACTCCCCCCACCCG 64. V6AAAACCCCACCCCCTTTCCAAAGCCG 65. V7 AAAACCCCCGCCGGGACCCCGCCCCG 66. V8AAAACCAGCGCCACGACCTCCGAGCG 67. V9 AAAACAGCGCCCTGGCCGGTGAGTCG 68. V10AAAACGTCCACCTAACCGCTGCGCCG 69. V11 AAAACGCGGGGCGGAGCCATGCGCCG 70. V12AAAACGGTAGCTCGGAGGTCGTGGCG 71. V13 AAAACAGGGGGAGGGCTCACGCCGCG 72. V14AAAACACCCCCTCCACCCCGCCTCCG 73. V15 AAAACCCGGAGCGCGGCGTGAGCCCG 74. V16AAAACGAGGCGGGGTGGAGGGGGTCG 75. Ni AAAACGGCCAGATGGCTCCGCGCTCG 76. N2AAAACTAACCCCTTCCGCGCCGCGCG 77. N3 AAAACGCCGGCCCGCGCCGCGCCGCG 78. N4AAAACGCGGGGGAGGGCGGCGCGGCG 79. N5 AAAACGGTTGGCTGGTTATAACCGCG 80. N6AAAACTTCCGAACAGCTCCGCGCACG 81.These fragments were ligated into BsmBI-digested plasmid pMLM3636 toyield DNA encoding a chimeric ˜102 nt single-chain guide RNA (Mali etal., Science. 2013 Feb. 15; 339(6121):823-6; Hwang et al., NatBiotechnol. 2013 March; 31(3):227-9) expressed by a human U6 promoter.The pMLM3636 plasmid and its full DNA sequence are available fromAddgene. See FIG. 4.

To engineer a Cas9-activator the D10A, H840A catalytic mutations(previously described in Jinek et al., 2012; and Qi et al., 2013) wereintroduced into either the wild-type or a codon-optimized Cas9 sequence(FIG. 5). These mutations render the Cas9 catalytically inactive so thatit will no longer induce double-strand breaks. In one construct, atriple flag tag, nuclear localization signal and the VP64 activationdomain were fused to the C-terminus of the inactive Cas9 (FIG. 6).Expression of this fusion protein was driven by the CMV promoter.

Construction of dCas-VP64 expression plasmids was performed as follows.DNA encoding the Cas9 nuclease harboring inactivating D10A/H840Amutations (dCas9) was amplified by PCR from plasmid pMJ841 (Addgeneplasmid #39318) using primers that add a T7 promoter site 5′ to thestart codon and a nuclear localization signal at the carboxy-terminalend of the Cas9 coding sequences and cloned into a plasmid containing aCMV promoter as previously described (Hwang et al., Nat Biotechnol 31,227-229 (2013)) to yield plasmid pMLM3629. Oligonucleotides encoding atriple FLAG epitope were annealed and cloned into XhoI and PstI sites inplasmid pMLM3629 to generate plasmid pMLM3647 expressing dCas9 with aC-terminal flag FLAG tag. DNA sequence encoding a Gly₄Ser linkerfollowed by the synthetic VP64 activation domain was introduceddownstream of the FLAG-tagged dCas9 in plasmid pMLM3647 to yield plasmidpSL690. The D10A/H840A mutations were also introduced by QuikChangesite-directed mutagenesis (Agilent) into plasmid pJDS247, which encodesa FLAG-tagged Cas9 sequence that has been codon optimized for expressionin human cells, to yield plasmid pMLM3668. DNA sequence encoding theGly₄Ser linker and the VP64 activation domain were then cloned intopMLM3668 to yield a codon-optimized dCas9-VP64 expression vector namedpMLM3705.

Cell Culture, Transfection and ELISA Assays were performed as follows.Flp-In T-Rex 293 cells were maintained in Advanced DMEM supplementedwith 10% FBS, 1% penstrep and 1% Glutamax (Invitrogen). Cells weretransfected by Lipofectamine LTX (Invitrogen) according tomanufacturer's instructions. Briefly, 160,000 293 cells were seeded in24-well plates and transfected the following day with 250 ng gRNAplasmid, 250 ng Cas9-VP64 plasmid, 30 ng pmaxGFP plasmid (Lonza), 0.5 ulPlus Reagent and 1.65 ul Lipofectamine LTX. Tissue culture media fromtransfected 293 cells was harvested 40 hours after transfection, andsecreted VEGF-A protein assayed using R&D System's Human VEGF-A ELISAkit “Human VEGF Immunoassay.”

16 sgRNAs were constructed for target sequences within three DNase Ihyper-sensitive sites (HSSs) located upstream, downstream or at thetranscription start site of the human VEGFA gene in 293 cells (FIG. 1E).

Before testing the abilities of the 16 VEGFA-targeted gRNAs to recruit anovel dCas9-VP64 fusion protein, each of these gRNAs was first assessedfor its ability to direct Cas9 nuclease to its intended target site inhuman 293 cells. For this purpose, gRNA and Cas9 expression vectors weretransfected in a 1:3 ratio because previous optimization experimentsdemonstrated a high level of Cas9-induced DNA cleavage in U2OS cellsusing this ratio of plasmids.

Transfections of 293 cells were performed as described above for thedCas9-VP16 VEGFA experiments except that cells were transfected with 125ng of plasmid encoding VEGFA-targeted gRNAs and 375 ng of plasmidencoding active Cas9 nuclease (pMLM3639). 40 hours post-transfection,genomic DNA was isolated using the QIAamp DNA Blood Mini kit (Qiagen)according to manufacturer's instructions. PCR amplification of the threedifferent targeted regions in the VEGFA promoter was performed usingPhusion Hot Start II high-fidelity DNA polymerase (NEB) with 3% DMSO andthe following touchdown PCR cycle: 10 cycles of 98° C., 10 s; 72-62° C.,−1° C./cycle, 15 s; 72° C., 30 s, followed by 25 cycles of 98° C., 10 s;62° C., 15 s; 72° C., 30 s. The −500 region was amplified using primersoFYF434 (5′-TCCAGATGGCACATTGTCAG-3′ (SEQ ID NO:82)) and oFYF435(5′-AGGGAGCAGGAAAGTGAGGT-3′ (SEQ ID NO:83)). The region around thetranscription start site was amplified using primers oFYF438(5′-GCACGTAACCTCACTTTCCT-3′ (SEQ ID NO:84)) and oFYF439(5′-CTTGCTACCTCTTTCCTCTTTCT-3′ (SEQ ID NO:85)). The +500 region wasamplified using primers oFYF444 (5′-AGAGAAGTCGAGGAAGAGAGAG-3′ (SEQ IDNO:86)) and oFYF445 (5′-CAGCAGAAAGTTCATGGTTTCG-3′ (SEQ ID NO:87)). PCRproducts were purified using Ampure XP beads (Agencourt) and T7Endonuclease I assays were performed and analyzed on a QIAXCEL capillaryelectrophoresis system as previously described (Reyon et al., NatBiotech 30, 460-465 (2012)).

All 16 gRNAs were able to mediate the efficient introduction of Cas9nuclease-induced indel mutations at their respective target sites asassessed using a previously described T7E1 genotyping assay (Table 2).Thus all 16 gRNAs can complex with Cas9 nuclease and direct its activityto specific target genomic sites in human cells.

TABLE 2 Frequencies of indel mutations induced by VEGFA-targeted gRNAsand Cas9 nuclease Mean Indel Mutation Frequency gRNA (%) ± SEM V1 18.05± 0.47 V2 41.48 ± 0.62 V3 33.22 ± 1.05 V4 16.97 ± 0.06 V5  7.46 ± 0.50V6 16.99 ± 0.51 V7  1.42 ± 0.11 V8 34.07 ± 0.90 V9 24.53 ± 1.40 V1035.65 ± 1.35 V11  4.45 ± 0.22 V12 23.95 ± 0.41 V13  9.45 ± 0.74 V1412,17 ± 0.36 V15 14.28 ± 0.54 V16 18.82 ± 1.48

To test whether dCas9-VP64 protein could also be targeted to specificgenomic sites in human cells by these same gRNAs, Enzyme-LinkedImmunoblot Assays of VEGFA protein were performed as follows. Culturemedium of Flp-In T-Rex HEK293 cells transfected with plasmids encodingVEGFA-targeted sgRNA and dCas9-VP64 was harvested 40 hourspost-transfection and VEGFA protein expression was measured by ELISA aspreviously described (Maeder et al., Nat Methods 10, 243-245 (2013)).Fold-activation of VEGFA expression was calculated by dividing theconcentration of VEGFA protein in media from cells in which both a sgRNAand dCas9-VP64 were expressed by the concentration of VEGFA protein inmedia from cells in which an off-target sgRNA (targeted to a sequence inthe EGFP reporter gene) and dCas9-VP64 were expressed.

15 of the 16 gRNAs tested induced significant increases in VEGFA proteinexpression when co-expressed with dCas9-VP64 in human 293 cells (FIG.2A). The magnitude of VEGFA induction observed ranged from two- to18.7-fold-activation with a mean of five-fold-activation. Controlexperiments revealed that expression of each of the 16 gRNAs alone,dCas9-VP64 alone, and dCas9-VP64 together with an “off-target” gRNAdesigned to bind an EGFP reporter gene sequence all failed to induceelevated VEGFA expression (FIG. 2A), demonstrating that co-expression ofa specific gRNA and the dCas9-VP64 protein are both required forpromoter activation. Thus dCas9-VP64 is stably expressed and can bedirected by gRNAs to activate transcription of specific genomic loci inhuman cells. The greatest increase in VEGFA was observed in cellstransfected with gRNA3, which induced protein expression by 18.7-fold.Interestingly, the three best gRNAs, and 6 of the 9 gRNAs capable ofinducing expression by 3-fold or more, target the −500 region (˜500 bpupstream of the transcription start site).

Because in one aspect the system described herein uses variable gRNAs torecruit a common dCas9-VP64 activator fusion, one can envision that theexpression of multiple guide RNAs in a single cell might enablemultiplex or combinatorial activation of endogenous gene targets. Totest this possibility, 293 cells were transfected with dCas9-VP64expression plasmid together with expression plasmids for four gRNAs (V1,V2, V3, and V4) that each individually induced expression from the VEGFApromoter. Co-expression of all four gRNAs with dCas9-VP64 inducedsynergistic activation of VEGFA protein expression (i.e., afold-activation greater than the expected additive effects of eachindividual activator) (FIG. 2B). In addition, various combinations ofthree of these four activators also activated the VEGFA promotersynergistically (FIG. 2B). Because synergistic activation oftranscription is believed to result from the recruitment of multipleactivator domains to a single promoter, multiple gRNA/dCas9-VP64complexes are likely to be simultaneously binding to the VEGFA promoterin these experiments.

These experiments demonstrate that co-expression of a Cas9-HFD, e.g., aCas9-activator protein (harboring the VP64 transcriptional activationdomain) and a sgRNA with 20 nt of sequence complementarity to sites inthe human VEGF-A promoter in human HEK293 cells can result inupregulation of VEGF-A expression. Increases in VEGF-A protein weremeasured by ELISA assay and it was found that individual gRNAs canfunction together with a Cas9-activator fusion protein to increaseVEGF-A protein levels by up to −18-fold (FIG. 2A). Additionally, it waspossible to achieve even greater increases in activation throughtranscriptional synergy by introducing multiple gRNAs targeting varioussites in the same promoter together with Cas9-activator fusion proteins(FIG. 2B).

Example 2. Engineering CRISPR/Cas Activator System Targeting theEndogenous Human NTF3 Gene

To extend the generality of the present findings, we tested whether theRNA-guided activator platform could be used to induce the expression ofthe human NTF3 gene. To do this, six sgRNAs were designed to a predictedDNase I hypersensitive site (HSS) in the human NTF3 promoter andplasmids expressing each of these gRNAs were co-transfected with aplasmid encoding dCas9-VP64 protein that had been codon optimized forhuman cell expression (FIG. 3A).

All six gRNAs tested induced significant increases in NTF3 transcriptlevels as detected by quantitative RT-PCR (FIG. 3B). Althoughfold-activation values for these six RNA-guided activators could not beaccurately calculated (because basal levels of transcript wereessentially undetectable), the mean levels of activated NTF3 mRNAexpression varied over a four-fold range. Decreasing the amounts of gRNAand dCas9-VP64 expression plasmids transfected resulted in lessactivation of the NTF3 gene (FIG. 3B), demonstrating a cleardose-dependent effect.

In addition, 293 cells were co-transfected with dCas9-VP64 andNTF3-targeted gRNA expression plasmids alone and in single and doublecombinations. Relative expression of NTF3 mRNA was detected byquantitative RT-PCR and normalized to a GAPDH control (deltaCt×10⁴). Inall of these experiments the amount of each individual gRNA expressionplasmid used for transfection was the same. FIG. 3B shows that thismultiplex gRNA expression induced synergistic activation of NTF3 mRNAexpression by dCas9-VP64 protein.

Example 3. Engineering CRISPR/Cas-MS2, -Csy4 and -Lambda N FusionSystems—Creating Biological Tethers

Fusion proteins are made in which an MS2 coat protein, Csy4 nuclease(preferably catalytically inactive Csy4, e.g., the H29A mutant describedin Haurwitz et al. 329(5997):1355-8 (2010)), or the lambda N are fusedto the N- or C-terminus of the inactivated dCas9. MS2 and lambda N arebacteriophage proteins that bind to a specific RNA sequence, and thuscan be used as adapters to tether to the dCas9 protein a heterologousRNA sequence tagged with the specific MS2 or lambda N RNA bindingsequence. dCas9-MS2 fusions or dCas9-lambda N fusions are co-expressedwith chimeric long non-coding RNAs (lncRNAs) fused to the MS2 or lambdaN stem loop recognition sequence on either their 5′ or 3′ end. ChimericXist or chimeric RepA lncRNAs will be specifically recruited by thedCas9 fusions and the ability of this strategy to induce targetedsilencing will be assayed by measuring target gene expression. Thesystem will be optimized by testing various alterations to the coatproteins and chimeric RNAs. The N55K and deltaFG mutations to the MS2coat protein have been previously demonstrated to prevent proteinaggregation and increase affinity for the stem-loop RNA. Additionally,we will test the high-affinity C-loop RNA mutant reported to increaseaffinity for the MS2 coat protein. Exemplary sequences for the MS2 andlambda N proteins are given below; the MS2 functions as a dimer,therefore the MS2 protein can include a fused single chain dimersequence.

1. Exemplary Sequences for Fusions of Single MS2 Coat Protein (Wt, N55Kor deltaFG) to the N-Terminus or C-Terminus of the dCas9.

MS2 coat protein amino acid sequence: (SEQ ID NO: 88)MASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY MS2 N55K: (SEQ ID NO: 89)MASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQKRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY MS2deltaFG: (SEQ ID NO: 90)MASNFTQFVLVDNGGTGDVTVAPSNFANGIAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKGAWRSYLNMELTIPIFATNSDCELIVKAMQG LLKDGNPIPSAIAANSGIY2. Exemplary Sequences for Fusions of Fused Dimeric MS2 Coat Protein(Wt, N55K or deltaFG) to the N-Terminus or C-Terminus of dCas9.

Dimeric MS2 coat protein: (SEQ ID NO: 91MASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGLYGAMASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLL KDGNPIPSAIAANSLIN(SEQ ID NO: 92) MASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQKRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGLYGAMASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQKRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLL KDGNPIPSAIAANSLINDimeric MS2deltaFG: (SEQ ID NO: 93)MASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQKRKYTIKVEVPKGAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGLYGAMASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQKRKYTIKVEVPKGAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSLIN3. Exemplary Sequences for Fusions of Lambda N to N-Terminus orC-Terminus of dCas9.

Lambda N amino acid sequence: (SEQ ID NO: 94) MDAQTRRRERRAEKQAQWKAAN or(SEQ ID NO: 95) MDAQTRRRERRAEKQAQWKAANPLLVGVSAKPVNRPILSLNRKPKSRVESALNPIDLTVLAEYHKQIESNLQRIERKNQRTWYSKPGERGITCSGRQK IKGKSIPLI4. Exemplary Sequence for Fusions of Csy4 to N-Terminus or C-Terminus ofdCas9

Exemplary sequences for Cys4 are given in Haurwitz et al.329(5997):1355-8 (2010), e.g., the inactivated form.

The constructs are expressed in cells also expressing a regulatory RNA,e.g., a long non-coding RNA (lncRNA) such as HOTAIR, HOTTIP, XIST orXIST RepA, that has been fused with the cognate stem-loop recognitionsequence for the lambda N or MS2 on either its 5′ or 3′ end. The wildtype and high-affinity sequences for MS2 are AAACAUGAGGAUUACCCAUGUCG(SEQ ID NO:96) and AAACAUGAGGAUCACCCAUGUCG (SEQ ID NO:97), respectively(see Keryer-Bibens et al., supra, FIG. 2); the nutL and nutR BoxBsequences to which lambda N binds are GCCCUGAAGAAGGGC (SEQ ID NO:98) andGCCCUGAAAAAGGGC (SEQ ID NO:99), respectively. The sequence to which Csy4binds is

(truncated 20 nt) (SEQ ID NO: 100) GTTCACTGCCGTATAGGCAG or(SEQ ID NO: 101) GUUCACUGCCGUAUAGGCAGCUAAGAAA.

The binding of the dCas9/MS2 to a target site in a cell expressing anMS2-binding sequence tagged lncRNA recruits that lncRNA to the dCas9binding site; where the lncRNA is a repressor, e.g., XIST, genes nearthe dCas9 binding site are repressed. Similarly, binding of thedCas9/lambdaN to a target site in a cell expressing an lambdaN-bindingsequence tagged lncRNA recruits that lncRNA to the dCas9 binding site.

Example 4. Engineering CRISPR/Cas-HP1 Fusion Systems—Sequence-SpecificSilencing

The dCas9 fusion proteins described herein can also be used to targetsilencing domains, e.g., Heterochromatin Protein 1 (HP1, also known asswi6), e.g., HP1α or HP10. Truncated versions of HP1α or HP1β in whichthe chromodomain has been removed can be targeted to specific loci toinduce heterochromatin formation and gene silencing. Exemplary sequencesof truncated HP1 fused to dCas9 are shown in FIGS. 8A-8B. The HP1sequences can be fused to the N- or C-terminus of the inactivated dCas9as described above.

Example 5. Engineering CRISPR/Cas-TET Fusion Systems—Sequence-SpecificDemethylation

The dCas9 fusion proteins described herein can also be used to targetenzymes that modify the methylation state of DNA (e.g., DNAmethyltransferase (DNMT) or TET proteins). Truncated versions of TET1can be targeted to specific loci to catalyze DNA demethylation.Exemplary sequences of truncated TET1 fused to dCas9 are shown in FIG.9. The TET1 sequence can be fused to the N- or C-terminus of theinactivated dCas9 as described above.

Example 6. Engineering Optimized CRISPR/Cas-VP64 Fusions

The activities of dCas9-based transcription activators harboring theVP64 activation domain were optimized by varying the number and positionof the nuclear localization signal(s) (NLS) and 3xFLAG-tags within thesefusions (FIG. 10). dCas9-VP64 fusions that contain both an N-terminalNLS and an NLS that lies between the dCas9 and VP64 sequencesconsistently induce higher levels of target gene activation, perhapsresulting from enhanced nuclear localization of the activator (FIG. 10).Furthermore, even greater levels of activation were observed when a3xFLAG tag was placed between the C-terminal end of dCas9 and theN-terminal end of VP64. The 3xFLAG tag may act as an artificial linker,providing necessary spacing between dCas9 and VP64 and perhaps allowingfor better folding of the VP64 domain (that may not be possible whenconstrained near dCas9) or better recognition of VP64 by transcriptionalmediator complexes that recruit RNA polymerase II. Alternatively, thenegatively charged 3xFLAG tag might also function as a fortuitoustranscriptional activation domain, enhancing the effects of the VP64domain.

Example 7. Optimized CatalyticallyCatlytically Inactive Cas9 Proteins(dCas9)

Additional optimization of the activities of dCas9-VP64 activators wasperformed by changing the nature of the inactivating mutations thatabolish the nuclease activity of Cas9 in the dCas9 domain (FIG. 11A-B).In published studies to date, the catalytic residues D10 and H840 weremutated to alanine (D10A and H840A) to disrupt the active site networksthat mediate the hydrolysis of DNA. It was hypothesized that alaninesubstitutions at these positions might result in destabilization ofdCas9 and therefore suboptimal activity. Therefore, more structurallyconservative substitutions at D10 or H840 (for example, to asparagine ortyrosine residues: D1 ON, H840N, and H840Y) were tested to see if theymight lead to greater gene activation by dCas9-VP64 fusions bearingthese different mutations. When dCas9-VP64 variants bearing thesevariant substitutions were co-transfected into HEK293 cells with threegRNAs targeting upstream regions of the endogenous human VEGFA gene,greater VEGFA protein expression was observed for all but one of thesevariants (FIG. 11A). However, this effect was not as significant whenthe dCas9-VP64 variants were co-transfected with only one of these gRNAs(FIG. 11A), or when transfected into a HEK293 derivative cell-line thatexpresses a single VEGFA-targeted gRNA (FIG. 11B).

OTHER EMBODIMENTS

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

1-25. (canceled)
 26. A method of silencing or repressing expression of atarget gene in a cell, the method comprising expressing (i) a fusionprotein comprising catalytically inactive CRISPR associated 9 (dCas9)protein linked to a heterologous functional domain, wherein theheterologous functional domain is a transcriptional silencer ortranscriptional repression domain, and (ii) one or more guide RNAsdirected to the target gene.
 27. The method of claim 26, wherein thetranscriptional repression domain is a Krueppel-associated box (KRAB)domain, ERF repressor domain (ERD), or mSin3A interaction domain (SID).28. The method of claim 26, wherein the transcriptional silencer is aHeterochromatin Protein 1 (HP1).
 29. The method of claim 26, wherein thecatalytically inactive Cas9 protein is from S. pyogenes.
 30. The methodof claim 26, wherein the catalytically inactive Cas9 protein comprisesmutations at D10, E762, H983, or D986; and at H840 or N863.
 31. Themethod of claim 30, wherein the mutations are: (i) D10A or D10N, and(ii) H840A, H840N, or H840Y.
 32. The method of claim 26, wherein theheterologous functional domain is linked to the N terminus or C terminusof the catalytically inactive Cas9 protein, with an optional interveninglinker, wherein the linker does not interfere with activity of thefusion protein.
 33. The method of claim 26, further comprising one orboth of a nuclear localization sequence and one or more epitope tags onthe N-terminus, C-terminus, and/or in between the catalytically inactiveCRISPR associated 9 (Cas9) protein and the heterologous functionaldomain, optionally with one or more intervening linkers.
 34. The methodof claim 33, wherein the epitope tag is c-myc, 6His, or FLAG.